More on output of geolocated TIFFs with transparency

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -486,6 +486,9 @@ public class CLTParameters {
 	public int        gmap_crop_extra =      20;
 	public int []     gmap_tex_pals =        {0,1,2};
 
+	public boolean    gmap_save_alt =        true;  // save height map (meters ASL)  
+	public boolean    gmap_save_tiff =       true;  // save transparent TIFF with geo metadata (top left corner)
+	public int        gmap_tiff_pal =        0;     // LWIR palette for TIFF  
 	
 	
 	public boolean    generate_bg =      true;  // Generate background image for 3dmodels

src/main/java/com/elphel/imagej/ims/Imx5.java

@@ -257,5 +257,15 @@ public class Imx5 {
 		return ned;
 	}
 
-	
+	/*
+	 * Offset Latitude, Longitude, Altitude by North, East, Up (in meters) 
+	 */
+	public static double [] offsetLla(double [] lla, double [] ned) {
+		double [] offset_lla = new double [] {
+				lla[0] + (ned[0]/EARTH_RADIUS / Math.PI * 180 / Math.cos(lla[0])), // degrees
+				lla[1] + (ned[1]/EARTH_RADIUS / Math.PI * 180), // degrees
+				lla[2] - ned[2]
+		};
+		return offset_lla;
+	}
 }

src/main/java/com/elphel/imagej/readers/ElphelTiffWriter.java

@@ -78,9 +78,8 @@ public class ElphelTiffWriter {
 			int           debugLevel
 			) {
 	    File outputFile = new File(path);
-	    if (debugLevel > 0) {
-	    	System.out.println("saveTiffARGB32(): will write to "+outputFile);
-	    	System.out.println("ElphelTiffWriter.saveTiffARGB32");
+	    if (debugLevel > -3) {
+	    	System.out.println("ElphelTiffWriter.saveTiffARGB32(): will write to "+outputFile);
 	    }
 	    ImageWriter tiffWriter = ImageIO.getImageWritersByFormatName("tiff").next();
 	    ImageWriteParam tiffWriteParam = tiffWriter.getDefaultWriteParam();

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

@@ -38,6 +38,7 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.nio.file.attribute.PosixFilePermission;
+import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -72,6 +73,7 @@ import com.elphel.imagej.ims.Did_ins_2;
 import com.elphel.imagej.ims.Did_pimu;
 import com.elphel.imagej.ims.EventLogger;
 import com.elphel.imagej.ims.Imx5;
+import com.elphel.imagej.readers.ElphelTiffWriter;
 import com.elphel.imagej.readers.ImagejJp4Tiff;
 import com.elphel.imagej.x3d.export.TriMesh;
 import com.elphel.imagej.x3d.export.WavefrontExport;
@@ -227,6 +229,13 @@ public class QuadCLTCPU {
 		return dxyzatyr;
 	}
 
+	public double [] getLla() {
+		return did_ins_2.lla;
+	}
+	
+	public LocalDateTime getLocalDateTime() {
+		return did_ins_2.getLocalDateTime();
+	}
 	public static double [][] scaleDtToErs(
 			CLTParameters clt_parameters,
 			double [][] cam_dxyzatr){
@@ -413,7 +422,7 @@ public class QuadCLTCPU {
     		double        discard_rdisp,  // discard above/below this fraction of average height
     		double        pix_size,       // in meters
     		int           max_image_width,// increase pixel size as a power of 2 until image fits
-    		double []     x0y0,        // initialize to double[2] to return width, height
+    		double []     x0y0,           // top level offset in meters
     		int []        whs,            // initialize to int[3] to return {width, height, scale reduction}
     		int debug_level
     		) {
@@ -745,7 +754,7 @@ public class QuadCLTCPU {
     			max_disparity,            // double    max_disparity,
     			discard_low,              // double    discard_low,    // fraction of all pixels
     			discard_high,             // double    discard_high,   // fraction of all pixels
-    			xy_range,                 // double [][] xy_range,     // should be double[2][];
+    			xy_range,                 // double [][] xy_range,     // should be double[2][]; meters
     			debug_level);             // int debug_level)
     	// camera position and orientation relative to the same lat/long on the ground below it 
 //    	double [][] scene_abs_xyzatr_enu = new double [][] {new double[] {0,0,-agl},	scene_abs_atr_enu};
@@ -3247,6 +3256,25 @@ public class QuadCLTCPU {
 		return imp;
 	}
 
+	public ImagePlus saveDoubleArrayInTopModelDirectory(
+			String      suffix,
+			String []   labels, // or null
+			double [][] data,
+			int         width,
+			int         height)
+	{
+		String x3d_path = getX3dTopDirectory();
+		String file_name = image_name + suffix;
+		String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
+		ImageStack imageStack = ShowDoubleFloatArrays.makeStack(data, width, height, labels);
+		ImagePlus imp = new ImagePlus( file_name, imageStack);
+		FileSaver fs=new FileSaver(imp);
+		fs.saveAsTiff(file_path);
+		System.out.println("saveDoubleArrayInModelDirectory(): saved "+file_path);
+		return imp;
+	}
+	
+	
 	public ImagePlus saveDoubleArrayInModelDirectory(
 			String      suffix,
 			double []   data,
@@ -16299,6 +16327,7 @@ public class QuadCLTCPU {
 				  suffix,
 				  debugLevel);
 	  }
+	  
 	  public boolean writeLwirPreview(
 			  final CLTParameters  clt_parameters,
 			  double []            data,
@@ -16315,7 +16344,6 @@ public class QuadCLTCPU {
 		  for (int i = 0; i < rendered_texture[0].length; i++) {
 			  rendered_texture[1][i] = Double.isNaN(rendered_texture[0][i])? 0.0: 1.0;
 		  }
-//		  double [] minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
 		  if (!suffix.equals("")) {
 			  if (minmax == null) { // to replace standard preview file name
 				  minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
@@ -16324,7 +16352,6 @@ public class QuadCLTCPU {
 				  suffix +="-RANGE"+(minmax[1]-minmax[0]);
 			  }
 		  }
-//		  int width = getTileProcessor().getTilesX() *getTileProcessor().getTileSize(); 
 		  int height = data.length/width;
 		  String set_name = getImageName();
 		  if (set_name == null ) {
@@ -16367,6 +16394,68 @@ public class QuadCLTCPU {
 		  return true;
 	  }
 	 
+	  public boolean writeLwirGeoTiffARGB(
+			  final CLTParameters  clt_parameters,
+			  double []            data,
+			  double []            lla,  // latitude, longitude, altitude (or null)
+			  LocalDateTime        dt,   // local date/time or null
+			  double               pix_in_meters,
+			  int                  width,
+			  double []            minmax, // null for auto
+			  QuadCLT              scene,
+			  int                  tex_palette,
+			  String               suffix, // include "-geo"
+			  int                  debugLevel) {
+		  if (scene == null) {
+			  scene = (QuadCLT) this;
+		  }
+		  double [][] rendered_texture = new double[][] {data, new double[data.length]};
+		  for (int i = 0; i < rendered_texture[0].length; i++) {
+			  rendered_texture[1][i] = Double.isNaN(rendered_texture[0][i])? 0.0: 1.0;
+		  }
+		  if (!suffix.equals("")) {
+			  if (minmax == null) { // to replace standard preview file name
+				  minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
+				  suffix +="-AUTORANGE";
+			  } else {
+				  suffix +="-RANGE"+(minmax[1]-minmax[0]);
+			  }
+		  }
+		  int height = data.length/width;
+		  String set_name = getImageName();
+		  if (set_name == null ) {
+			  QuadCLTCPU.SetChannels [] set_channels = setChannels(debugLevel);
+			  set_name = set_channels[0].set_name;
+		  }
+		  String model_dir= correctionsParameters.selectX3dDirectory(
+				  set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+				  null,
+				  true,  // smart,
+				  true);  //newAllowed, // save\
+		  String title = getImageName()+suffix;
+		  ImagePlus imp =  	  QuadCLTCPU.linearStackToColorLWIR(
+				  clt_parameters, // CLTParameters  clt_parameters,
+				  tex_palette, // int            lwir_palette, // <0 - do not convert
+				  minmax, // double []      minmax,
+				  title, // String         name,
+				  "", // String         suffix, // such as disparity=...
+				  true, // boolean        toRGB,
+				  rendered_texture, // faded_textures[nslice], // double [][]    texture_data,
+				  width, // int            width, // int tilesX,
+				  height, // int            height, // int tilesY,
+				  debugLevel); // int            debugLevel )
+		  String image_path = model_dir +  Prefs.getFileSeparator() + title+".tiff";
+		  ElphelTiffWriter.saveTiffARGB32(
+				  imp,
+				  image_path,
+				  lla,           // double []     lla,  // latitude, longitude, altitude (or null)
+				  dt,            // LocalDateTime dt,   // local date/time or null
+				  pix_in_meters, //double        pix_in_meters, // resolution or Double.NaN
+				  false,         // imageJTags,
+				  debugLevel);
+		  return true;
+	  }
+	  
 	  
 	/** broke  
 	  public boolean writeRatingFile( // USED in lwir

src/main/java/com/elphel/imagej/tileprocessor/TexturedModel.java

@@ -24,6 +24,7 @@ package com.elphel.imagej.tileprocessor;
 //import java.awt.Point;
 import java.awt.Rectangle;
 import java.io.IOException;
+import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -39,6 +40,7 @@ import com.elphel.imagej.common.DoubleGaussianBlur;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.correction.EyesisCorrections;
 import com.elphel.imagej.gpu.TpTask;
+import com.elphel.imagej.ims.Imx5;
 import com.elphel.imagej.x3d.export.GlTfExport;
 import com.elphel.imagej.x3d.export.Render3D;
 import com.elphel.imagej.x3d.export.TriMesh;
@@ -2468,6 +2470,10 @@ public class TexturedModel {
 		final boolean   crop_empty =      clt_parameters.gmap_crop_empty ; //true;
 		final int       crop_extra =      clt_parameters.gmap_crop_extra ; //20;
 		final int []    tex_pals =        clt_parameters.gmap_tex_pals ; //{0,1,2};
+		final boolean   gmap_save_alt =   clt_parameters.gmap_save_alt;  // true;  // save height map (meters ASL)  
+		final boolean   gmap_save_tiff =  clt_parameters.gmap_save_tiff; // true;  // save transparent TIFF with geo metadata (top left corner)
+		final int       gmap_tiff_pal =   clt_parameters.gmap_tiff_pal;  // 0;     // LWIR palette for TIFF  
+		
 		
 		final double  range_disparity_offset = clt_parameters.imp.range_disparity_offset;// double  range_disparity_offset
 		final boolean batch_mode =        clt_parameters.multiseq_run; // batch_run;
@@ -3046,15 +3052,15 @@ public class TexturedModel {
 							hdr_whs[0],            // int          out_width,    // output rendered image width in pixels
 							hdr_whs[1]);           // int          out_height);   // output rendered image height in pixels
 					boolean last_is_alpha = true; // last channel in textures slices is alpha
-					double [][] full_render;
+					double [][] full_render_z;
 					if (use_parallel_proj) {
-						full_render =render3D.render3dPlaneParallelProj(
+						full_render_z =render3D.render3dPlaneParallelProj(
 								tri_meshes,            // final ArrayList<TriMesh> tri_meshes,
 								last_is_alpha,         // final boolean            last_is_alpha,
 								//							scenes[ref_index],     //final QuadCLT            ref_scene,    // all coordinates relative to this scene
 								debugLevel);           //int                      debugLevel)
 					} else {
-						full_render =render3D.render3dPlaneCenterProj(
+						full_render_z =render3D.render3dPlaneCenterProj(
 								tri_meshes,            // final ArrayList<TriMesh> tri_meshes,
 								last_is_alpha,         // final boolean            last_is_alpha,
 								//						scenes[ref_index],     //final QuadCLT            ref_scene,    // all coordinates relative to this scene
@@ -3069,33 +3075,100 @@ public class TexturedModel {
 					scenes[ref_index].saveDoubleArrayInModelDirectory(
 							suffix+"-FULL", // String      suffix,
 							null, // String []   labels, // or null
-							full_render, // double [][] data,
+							full_render_z, // double [][] data, // including Z as it was
 							hdr_whs[0], // int            width, // int tilesX,
 							hdr_whs[1]); // int            height, // int tilesY,
+					double [][] img_cropped_z = full_render_z;
+//					int []  wh = hdr_whs.clone();
 					if (crop_empty || (crop_extra > 0)) {
-						int []  wh = new int[2];
-						double [][] img_cropped = Render3D.cropRectified(
+						int []  ltwh = new int[4];
+						img_cropped_z = Render3D.cropRectified(
 								crop_empty,    // boolean crop_empty,
-								last_is_alpha, // boolean last_is_alpha,
+//								last_is_alpha, // boolean last_is_alpha,
+								full_render_z.length - 2, // last is Z, previous is alpha
 								crop_extra,    // int     crop_extra,
 								hdr_whs[0],    // int     width,
-								wh,            // int []  wh, // should be initialized to int [2]
-								full_render);  // double [][] img_src) 
-						if (img_cropped != null) { // has NaN and alpha 0-1
-							scenes[ref_index].saveDoubleArrayInModelDirectory(
+								ltwh,            // int []  wh, // should be initialized to int [2]
+								full_render_z);  // double [][] img_src)
+						if (img_cropped_z != null) { // has NaN and alpha 0-1
+							hdr_whs[0] = ltwh[2]; // cropped width
+							hdr_whs[1] = ltwh[3]; // cropped height
+							hdr_x0y0[0] +=ltwh[0]* scaled_pixel_size; // meters corrected by pixels
+							hdr_x0y0[1] +=ltwh[1]* scaled_pixel_size; // meters corrected by pixels
+							scenes[ref_index].saveDoubleArrayInModelDirectory( // save with Z
 									suffix+"-CROP", // String      suffix,
 									null,           // String []   labels, // or null
-									img_cropped,    // double [][] data,
-									wh[0],          // int            width, // int tilesX,
-									wh[1]);         // int            height, // int tilesY,
-							//				for (int tex_palette = tex_palette_start; tex_palette <= tex_palette_end; tex_palette++) {
+									img_cropped_z,    // double [][] data,
+									hdr_whs[0], // int            width, // int tilesX,
+									hdr_whs[1]); // int            height, // int tilesY,
+						} else {
+							img_cropped_z = full_render_z; // restore
+						}
+					}
+					// Here use cropped or full (non-cropped) if not calculated and save separately
+					// textures and altitude ASL
+					if (img_cropped_z != null) { // has NaN and alpha 0-1
+						double [][] img_cropped = new double [img_cropped_z.length - 1][];
+						for (int i = 0; i < img_cropped.length; i++) {
+							img_cropped[i] = img_cropped_z[i];
+						}
+						double [][] cropped_z = new double [][] {img_cropped_z[img_cropped_z.length-1].clone(), img_cropped_z[img_cropped_z.length-2]};
+						// scale units, add altitude, add NaNs
+						double [] ref_lla = scenes[ref_index].getLla();
+						if (ref_lla == null) {
+							ref_lla = new double[3];
+						}
+						// correct GPS coordinates to top-left corner of the result (full) image
+						double [] top_left_lla_offset_ned = new double[] {
+							hdr_x0y0[1], // North // hdr_x0y0 - in meters !
+							hdr_x0y0[0], // East
+							0}; // no altitude offset here
+						double [] top_left_lla = Imx5.offsetLla(ref_lla,top_left_lla_offset_ned);
+						int num_pix = 0;
+						double sum_z = 0.0;
+						for (int i = 0; i < cropped_z[0].length; i++) {
+							if (cropped_z[1][i] <= 0.0) {
+								cropped_z[0][i] = Double.NaN;
+							} else {
+								cropped_z[0][i] = ref_lla[2] - cropped_z[0][i] * scaled_pixel_size;
+								num_pix++;
+								sum_z += cropped_z[0][i]; 
+							}
+						}
+						double avg_z = sum_z/num_pix;
+						top_left_lla[2] = avg_z; // average altitude. Maybe keep drone altitude?
+						if (gmap_save_alt) {
+							scenes[ref_index].saveDoubleArrayInTopModelDirectory( // save with Z
+									suffix+"-ALT", // String      suffix,
+									null,          // String []   labels, // or null
+									new double[][] {cropped_z[0]},    // double [][] data,
+									hdr_whs[0],    // int            width, // int tilesX,
+									hdr_whs[1]);   // int            height, // int tilesY,
+						}
+						double [] minmax =  tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;				
+						if (gmap_save_tiff && (gmap_tiff_pal >=0)) {
+							LocalDateTime dt = scenes[ref_index].getLocalDateTime(); 
+							scenes[ref_index].writeLwirGeoTiffARGB(
+									clt_parameters,                     // final CLTParameters  clt_parameters,
+									img_cropped[0],                     // double []            data,
+									top_left_lla,                       // double []            lla,  // latitude, longitude, altitude (or null)
+									dt,                                 // LocalDateTime        dt,   // local date/time or null
+									scaled_pixel_size,                  // double               pix_in_meters,
+									hdr_whs[0],                         // int     width,
+									minmax,                             // double []            minmax, // null for auto
+									null,                               // QuadCLT              scene,
+									gmap_tiff_pal,                      // int                  tex_palette,
+									suffix+"-GEO"+"-PAL"+gmap_tiff_pal, // String               suffix,
+									debugLevel);                        // int                  debugLevel)
+						}
+						
 						for (int tex_palette: tex_pals) {
 							// try with fixed range?
-								double [] minmax =  tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;				
+//							double [] minmax =  tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;				
 							scenes[ref_index].writeLwirPreview(
 									clt_parameters, // final CLTParameters  clt_parameters,
 									img_cropped[0], // double []            data,
-										wh[0],          // int            width, // int tilesX,
+									hdr_whs[0],    // int     width,
 									minmax, // 			  double []            minmax, // null for auto
 									null, // QuadCLT              scene,
 									tex_palette, // int                  tex_palette,
@@ -3103,7 +3176,7 @@ public class TexturedModel {
 									debugLevel); // int                  debugLevel)
 						}
 					}
-					}
+
 				}
 			}
 		}

src/main/java/com/elphel/imagej/x3d/export/Render3D.java

@@ -137,20 +137,25 @@ public class Render3D {
 	
 	public static double [][] cropRectified(
 			boolean crop_empty,
-			boolean last_is_alpha,
+//			boolean last_is_alpha,
+			int     indx_alpha,
 			int     crop_extra,
 			int     width,
-			int []  wh, // should be initialized to int [2]
+			int []  ltwh, // should be initialized to int [4] (left,top,width, height)
 			double [][] img_src){
 		int height = img_src[0].length/width;
-		int indx_alpha = img_src.length - 1;
+//		int indx_alpha = img_src.length - 1;
 		int marg_top=0,marg_left=0,marg_bottom=0,marg_right=0;
 		if (crop_empty) {
 			int [][] xy_min_max= null; // new int[2][2];
 			for (int iy = 0; iy<height; iy++) {
 				for (int ix=0; ix<width; ix++) {
 					int indx=iy * width +ix;
-					if (last_is_alpha? (img_src[indx_alpha][indx] > 0.0) : !Double.isNaN(img_src[0][indx])) {
+//					if (last_is_alpha? (img_src[indx_alpha][indx] > 0.0) : !Double.isNaN(img_src[0][indx])) {
+					if (!Double.isNaN(img_src[0][indx])) {
+						if ((indx_alpha >= 0) && (img_src[indx_alpha][indx] <= 0.0)) {
+							continue;
+						}
 						if (xy_min_max == null) {
 							xy_min_max=new int [][] {{ix,ix},{iy,iy}};
 						} else {
@@ -176,8 +181,10 @@ public class Render3D {
 		marg_right +=   crop_extra;
 		int out_width =  width - marg_left - marg_right;
 		int out_height = height - marg_top - marg_bottom;
-		wh[0] = out_width;
-		wh[1] = out_height;
+		ltwh[0] = marg_left;
+		ltwh[1] = marg_top;
+		ltwh[2] = out_width;
+		ltwh[3] = out_height;
 		double [][] img_cropped = new double [img_src.length][out_width*out_height];
 		for (int row = 0; row < out_height; row++) {
 			for (int chn = 0; chn < img_cropped.length; chn++) {